4HCO

Human Plk1-PBD in complex with Thymoquinone at the phophopeptide binding site

Structural Biology Knowledgebase: 4HCO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4HCO

Classification: TRANSFERASE / TRANSFERASE INHIBITOR

Total Structure Weight: 55345.30

Macromolecule Entities
Molecule Chains Length Organism Details
Serine/threonine-protein kinase PLK1 A, B 240 Homo sapiens EC#: 2.7.11.21 IUBMB
Fragment: UNP residues 367-603
Gene Name(s): PLK1 Gene View PLK

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
IMW
Query on IMW

A 2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene- 1,4-dione
Thymoquinone, 2-isopropyl-5-methylbenzo-1,4- quinone (Synonym)
C10 H12 O2
KEQHJBNSCLWCAE-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IMW N/A in BindingDB
N/A in BindingMoad
IC50: 47380 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.206
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 33.26 α = 90.00
b = 102.15 β = 93.96
c = 67.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-01
  • Released Date: 2012-10-10
  • Deposition author(s): Yin, Z., Rehse, P.H.
  • Previous versions: 3MQ8 4H70

Revision History

  • 2013-03-06
    Type: Citation | Details: Citation update